Repositories list

• MMseqs2-App

  Public

  soedinglab/MMseqs2-App’s past year of commit activity
  MMseqs2 app to run on your workstation or servers

  electrondockergolang+ 10

  electrondockergolangbioinformaticsvuedocker-composeprofile-searchsequence-searchmmseqsalphafold2+ 3

  Vue

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  GNU General Public License v3.0

  •3131 forks•108108 stars•1616 issues•1212 pull requests•Updated Apr 23, 2026Apr 23, 2026

• PMGen

  Public

  soedinglab/PMGen’s past year of commit activity
  peptide-MHC modeling, binding prediction, and protein design.

  Python

  •

  Apache License 2.0

  •44 forks•2525 stars•00 issues•11 pull request•Updated Apr 21, 2026Apr 21, 2026

• phylo_grad

  Public

  soedinglab/phylo_grad’s past year of commit activity
  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•33 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• MMseqs2

  Public

  soedinglab/MMseqs2’s past year of commit activity
  MMseqs2: ultra fast and sensitive search and clustering suite

  bioinformaticstaxonomymetagenomics+ 7

  bioinformaticstaxonomymetagenomicsalignmentsequence-clusteringprofile-searchsequence-searchlinclustmmseqsblast

  C

  •

  MIT License

  •282282 forks•2k2k stars•487487 issues•2323 pull requests•Updated Apr 16, 2026Apr 16, 2026

• binning_benchmarking

  Public
  Jupyter Notebook

  •00 forks•1111 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• MAGmax

  Public
  From dereplication to genome enrichment: Enhancing genome recovery across metagenomic samples using MAGmax

  Rust

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  GNU General Public License v3.0

  •33 forks•2727 stars•11 issue•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• MMseqs2-Regression

  Public
  MMseqs2 Regression Testing

  Shell

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  GNU General Public License v3.0

  •55 forks•22 stars•00 issues•22 pull requests•Updated Apr 3, 2026Apr 3, 2026

• LoLalign-analysis

  Public

  soedinglab/LoLalign-analysis’s past year of commit activity
  Scripts for Reproducing LoL-align Benchmarks

  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 27, 2026Feb 27, 2026

• spacedust

  Public

  soedinglab/spacedust’s past year of commit activity
  Discovery of conserved gene clusters in multiple genomes

  C

  •

  GNU General Public License v3.0

  •66 forks•129129 stars•2020 issues•00 pull requests•Updated Jan 16, 2026Jan 16, 2026

• metaeuk

  Public

  soedinglab/metaeuk’s past year of commit activity
  MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

  bioinformaticsmetagenomicsgene-prediction+ 2

  bioinformaticsmetagenomicsgene-predictioneukaryotesgene-discovery

  C

  •

  GNU General Public License v3.0

  •2525 forks•204204 stars•2727 issues•00 pull requests•Updated Aug 25, 2025Aug 25, 2025

• b-lore

  Public
  Bayesian multiple logistic regression for GWAS meta-analysis

  C++

  •

  GNU General Public License v3.0

  •22 forks•1717 stars•00 issues•11 pull request•Updated Aug 20, 2025Aug 20, 2025

• hhdatabase_pfam

  Public
  Scripts to generate the pfam database for hh-suite

  Shell

  •00 forks•00 stars•22 issues•00 pull requests•Updated Aug 12, 2025Aug 12, 2025

• hh-suite

  Public
  Remote protein homology detection suite.

  opensourcebioinformaticscpp+ 11

  opensourcebioinformaticscppprotein-structuresimdalignmentprofile-searchsequence-searchhh-suitehhblits+ 4

  C

  •

  GNU General Public License v3.0

  •149149 forks•617617 stars•169169 issues•77 pull requests•Updated Aug 12, 2025Aug 12, 2025

• McDevol

  Public
  Python

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  GNU General Public License v3.0

  •00 forks•77 stars•11 issue•11 pull request•Updated Feb 24, 2025Feb 24, 2025

• transannot

  Public
  TransAnnot - a fast transcriptome annotation pipeline

  bioinformaticsannotationassembly+ 2

  bioinformaticsannotationassemblybioinformatics-pipelinetranscriptomics

  C

  •

  GNU General Public License v3.0

  •22 forks•2020 stars•66 issues•11 pull request•Updated Jan 22, 2025Jan 22, 2025

• plass

  Public
  sensitive and precise assembly of short sequencing reads

  opensourcebioinformaticsproteins+ 4

  opensourcebioinformaticsproteinsmetagenomicsproteomicssequence-assemblermetatranscriptomics

  C

  •

  GNU General Public License v3.0

  •1515 forks•166166 stars•3737 issues•00 pull requests•Updated Oct 11, 2024Oct 11, 2024

• WIsH

  Public
  Predict prokaryotic host for phage metagenomic sequences

  C++

  •

  GNU General Public License v3.0

  •1010 forks•5555 stars•33 issues•00 pull requests•Updated Sep 17, 2024Sep 17, 2024

• pdbx

  Public
  pdbx is a parser module in python for structures of the protein data bank in the mmcif format

  Python

  •77 forks•3030 stars•22 issues•00 pull requests•Updated Aug 9, 2024Aug 9, 2024

• spacepharer

  Public
  SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

  bioinformaticscrisprsequence-analysis+ 1

  bioinformaticscrisprsequence-analysishost-pathogen

  C

  •

  GNU General Public License v3.0

  •44 forks•4747 stars•77 issues•00 pull requests•Updated May 8, 2024May 8, 2024

• metaeuk-regression

  Public
  Regression test suite for MetaEuk

  Perl

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 1, 2024May 1, 2024

• prosstt

  Public
  PRObabilistic Simulations of ScRNA-seq Tree-like Topologies

  Python

  •

  GNU General Public License v3.0

  •99 forks•2525 stars•00 issues•22 pull requests•Updated Jan 10, 2024Jan 10, 2024

• CCMpred

  Public
  Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.

  C

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  GNU Affero General Public License v3.0

  •2828 forks•114114 stars•2020 issues•22 pull requests•Updated Nov 8, 2023Nov 8, 2023

• cooperative_rbp

  Public
  Python

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  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 13, 2023Sep 13, 2023

• art_marzooplclk

  Public
  Accompanying repository for the publication "RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton"

  bioinformatics

  bioinformatics

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 4, 2023Jan 4, 2023

• tejaas

  Public
  Tejaas - a tool for discovering trans-eQTLs

  gene-expressiongtexeqtl+ 3

  gene-expressiongtexeqtleqtl-mappingtrans-eqtlreverse-regression

  C

  •

  GNU General Public License v3.0

  •00 forks•1111 stars•22 issues•00 pull requests•Updated Oct 14, 2022Oct 14, 2022

• CoCo

  Public
  Consensus Correction

  C++

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  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 23, 2022Apr 23, 2022

• bmf-webserver

  Public
  Web server for Bipartite Motif Finder (BMF)

  Python

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  GNU Affero General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 16, 2022Jan 16, 2022

• contactpred-felsenstein

  Public
  Felsenstein implementation for phylogeny correction

  C

  •

  GNU General Public License v3.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Aug 29, 2021Aug 29, 2021

• CCMgen

  Public
  dcacontact-prediction

  dcacontact-prediction

  HTML

  •

  GNU Affero General Public License v3.0

  •99 forks•2020 stars•55 issues•11 pull request•Updated Jul 16, 2021Jul 16, 2021

• bmf-paper

  Public
  Notebooks to reproduce the analyses in BMF manuscript

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2021Mar 25, 2021